Structural and functional restraints in the evolution of protein families and superfamilies

Biochemical Society Transactions

Volumn 37, Issue 4, 2009, Pages 727-733

  Gong, Sungsam ^a   Worth, Catherine L ^a,b   Bickerton, G Richard J ^a,c   Lee, Semin ^a   Tanramluk, Duangrudee ^a   Blundell, Tom L ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b LEIBNIZ INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE   (Germany)

^c UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Buried residue; Hydrogen bond; Local structural environment; Protein evolution; Protein structure

Indexed keywords

CONFERENCE PAPER; EXPRESSED SEQUENCE TAG; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN NUCLEIC ACID INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; AMINO ACID SEQUENCE; CHEMISTRY; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; REVIEW; SEQUENCE HOMOLOGY;

NUCLEIC ACID; PROTEIN;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; HYDROGEN BONDING; MOLECULAR SEQUENCE DATA; NUCLEIC ACIDS; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 70349314263     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0370727     Document Type: Conference Paper

References (34)

1. Bajaj, M. and Blundell, T. (1984) Evolution and the tertiary structure of proteins. Annu. Rev. Biophys. Bioeng. 13, 453-492
2. Orengo, C.A. and Thornton, J.M. (2005) Protein families and their evolution: a structural perspective. Annu. Rev. Biochem. 74, 867-900
3. Sanger, F. and Tuppy, H. (1951) The amino-acid sequence in the phenylalanyl chain of insulin. 2. The investigation of peptides from enzymic hydrolysates. Biochem. J. 49, 481-490
4. Sanger, F. and Tuppy, H. (1951) The amino-acid sequence in the phenylalanyl chain of insulin. I. The identification of lower peptides from partial hydrolysates. Biochem. J. 49, 463-481
5. Sanger, F. (1988) Sequences, sequences, and sequences. Annu. Rev. Biochem. 57, 1-29
6. Adams, M.J., Blundell, T.L., Dodson, E.J., Dodson, G.G., Vijayan, M., Baker, E.N., Harding, M.M., Hodgkin, D.C., Rimmer, B. and Sheat, S. (1969) Structure of rhombohedral 2 zinc insulin crystals. Nature 224, 491-495
7. Blundell, T.L., Cutfield, J.F., Cutfield, S.M., Dodson, E.J., Dodson, G.G., Hodgkin, D.C., Mercola, D.A. and Vijayan, M. (1971) Atomic positions in rhombohedral 2-zinc insulin crystals. Nature 231, 506-511
8. Blundell, T.L., Cutfield, J.F., Cutfield, S.M., Dodson, E.J., Dodson, G.G., Hodgkin, D.C. and Mercola, D.A. (1972) Three-dimensional atomic structure of insulin and its relationship to activity. Diabetes 21, 492-505
9. Blundell, T.L. and Wood, S.P. (1975) Is the evolution of insulin Darwinian or due to selectively neutral mutation? Nature 257, 197-203
10. Kimura, M. (1968) Evolutionary rate at the molecular level. Nature 217, 624-626
11. Blundell, T.L. and Humbel, R.E. (1980) Hormone families: pancreatic hormones and homologous growth factors. Nature 287, 781-787
12. Slingsby, C., Driessen, H.P., Mahadevan, D., Bax, B. and Blundell, T.L. (1988) Evolutionary and functional relationships between the basic and acidic β-crystallins. Exp. Eye Res. 46, 375-403
13. Wistow, G., Summers, L. and Blundell, T. (1985) Myxococcus xanthus spore coat protein S may have a similar structure to vertebrate lens βγ-crystallins. Nature 315, 771-773
14. Blundell, T.L., Jenkins, J.A., Sewell, B.T., Pearl, L.H., Cooper, J.B., Tickle, I.J., Veerapandian, B. and Wood, S.P. (1990) X-ray analyses of aspartic proteinases: the three-dimensional structure at 2.1 Å resolution of endothiapepsin. J. Mol. Biol. 211, 919-941
15. Tang, J., James, M.N., Hsu, I.N., Jenkins, J.A. and Blundell, T.L. (1978) Structural evidence for gene duplication in the evolution of the acid proteases. Nature 271, 618-621
16. Blundell, T.L., Lapatto, R., Wilderspin, A.F., Hemmings, A.M., Hobart, P.M., Danley, D.E. and Whittle, P.J. (1990) The 3-D structure of HIV-1 proteinase and the design of antiviral agents for the treatment of AIDS. Trends Biochem. Sci. 15, 425-430
17. Luthy, R., McLachlan, A.D. and Eisenberg, D. (1991) Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10, 229-239
18. Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L. (1992) Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci. 1, 216-226
19. Overington, J., Johnson, M.S., Sali, A. and Blundell, T.L. (1990) Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc. Biol. Sci. 241, 132-145
20. Koshi, J.M. and Goldstein, R.A. (1995) Context-dependent optimal substitution matrices. Protein Eng. 8, 641-645
21. Levitt, M. (1978) Conformational preferences of amino acids in globular proteins. Biochemistry 17, 4277-4285
22. Worth, C.L. and Blundell, T.L. (2009) Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains. Proteins 75, 413-429
23. Hotelling, H. (1933) Analysis of complex statistical variables into principal components. J. Educ. Psychol. 24, 417-441
24. Hubbard, T.J. and Blundell, T.L. (1987) Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. 1, 159-171
25. Ofran, Y. and Rost, B. (2003) Analysing six types of protein-protein interfaces. J. Mol. Biol. 325, 377-387
26. Lee, S. and Blundell, T.L. (2009) Ulla: a program for calculating environment-specific amino acid substitution tables. Bioinformatics, doi:10.1093/bioinformatics/btp300
27. Shi, J., Blundell, T.L. and Mizuguchi, K. (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243-257
28. Gong, S. and Blundell, T.L. (2008) Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. PLoS Comput. Biol. 4, e1000179
29. Tanramluk, D., Schreyer, A., Pitt, W.R. and Blundell, T.L. (2009) On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine. Chem. Biol. Drug Des. 74, 16-24
30. Mizuguchi, K., Deane, C.M., Blundell, T.L., Johnson, M.S. and Overington, J.P. (1998) JOY: protein sequence-structure representation and analysis. Bioinformatics 14, 617-623
31. Lee, S. and Blundell, T.L. (2009) BIPA: a database for protein-nucleic acid interaction in 3D structures. Bioinformatics 25, 1559-1560
32. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882
33. Fabian, M.A., Biggs, 3rd, W.H., Treiber, D.K., Atteridge, C.E., Azimioara, M.D., Benedetti, M.G., Carter, T.A., Ciceri, P., Edeen, P.T., Floyd, M. et al. (2005) A small molecule-kinase interaction map for clinical kinase inhibitors. Nat. Biotechnol. 23, 329-336
34. Letunic, I. and Bork, P. (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127-128